Figure 6.

Typical duplex formation pathways for panels (A) and (B) P₃T₃, and panel (C) P₄T₄. Schematic illustrations below each figure indicate hairpin and duplex base pairs present. In panel (A) one intended and one non-intended 3-stem base pair are present just before and after the association event ((i) and (ii)) but have melted by the time the system has formed 15 inter-strand base pairs (iii). In panel (B) both intended 3-stem base pairs are present just before and after the association event ((i) and (ii)), and are still present even once the system has formed 15 inter-strand base pairs (iv). These hairpins must melt before the duplex can be formed (v). In panel (C) both intended 4-stem base pairs are present in (i)-(iii), but have melted by the time the system has formed 15 inter-strand base pairs (iv). The black nucleotides indicate the 3′ end of the strand. Gray nucleotides indicate the locations of the 3-base pair or 4-base pair hairpins present during the association event. The notation (1,6), for example, refers to 1 inter-strand and 6 intra-strand base pairs in the system.